Citrus Sinensis ID: 042175

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
MKTKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDNVN
cccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccHHHHHHHHHHcHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHcHHHHcccccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccc
cccccccHHHHHHHHHHHHHHHcccccEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcHEEEEEHcHcEccccHHccccccHHHHccccccHHHccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccc
mktknvspDRLLRAIVEMSSAigseglaagqimdissegkdvslselnfIHRHKSEKFVEASIVSGviigggneEEIERMRNYGKCVGMAYQLWNDIVDvigspetkettgrdmlrgkatypklvgidESKNYAKELLAKAKQElayfdpakaapldhLVNFMVSFDNVN
mktknvspdrlLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRhksekfveasivsgviigggneeeIERMRNYGKCVGMAYQLWNDIVDVIGSpetkettgrdmlrgkatypklvgidESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDNVN
MKTKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEAsivsgviigggneeeieRMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDNVN
******************************************SLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGS************RGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSF****
*****VSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN**
********DRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDNVN
****NVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKTKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDNVN
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query170 2.2.26 [Sep-21-2011]
Q42698357 Geranylgeranyl pyrophosph N/A no 0.976 0.464 0.470 8e-42
Q94ID7370 Geranylgeranyl pyrophosph N/A no 0.988 0.454 0.464 5e-40
Q43133366 Geranylgeranyl pyrophosph N/A no 0.976 0.453 0.470 1e-39
P34802371 Heterodimeric geranylgera yes no 0.958 0.439 0.461 1e-38
Q9LUD9360 Geranylgeranyl pyrophosph no no 0.958 0.452 0.461 1e-37
Q9ZU77347 Geranylgeranyl pyrophosph no no 0.958 0.469 0.443 1e-37
P80042369 Geranylgeranyl pyrophosph N/A no 0.976 0.449 0.440 2e-37
Q9LRR0361 Putative geranylgeranyl p no no 0.929 0.437 0.450 3e-37
Q9LUE1360 Geranylgeranyl pyrophosph no no 0.958 0.452 0.443 2e-36
O04046376 Heterodimeric geranylgera no no 0.958 0.433 0.455 2e-36
>sp|Q42698|GGPPS_CATRO Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Catharanthus roseus GN=GGPS1 PE=3 SV=1 Back     alignment and function desciption
 Score =  169 bits (428), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 79/168 (47%), Positives = 120/168 (71%), Gaps = 2/168 (1%)

Query: 3   TKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEG-KDVSLSELNFIHRHKSEKFVEA 61
           TK VS +R++R + E++  IGSEGL AGQ++D+ SEG  DV L  L FIH HK+   +E 
Sbjct: 190 TKGVSSERIVRVVGELAKCIGSEGLVAGQVVDVCSEGIADVGLEHLEFIHIHKTAALLEG 249

Query: 62  SIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVI-GSPETKETTGRDMLRGKAT 120
           S+V G I+GG N+E+I ++R + +C+G+ +Q+ +DI+DV   S E  +T G+D++  K T
Sbjct: 250 SVVLGAIVGGANDEQISKLRKFARCIGLLFQVVDDILDVTKSSQELGKTAGKDLVADKVT 309

Query: 121 YPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN 168
           YPKL+GID+S+ +A++L  +A+++LA FDP KAAPL  L N++   DN
Sbjct: 310 YPKLLGIDKSREFAEKLNREAQEQLAEFDPEKAAPLIALANYIAYRDN 357
Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate.
Catharanthus roseus (taxid: 4058)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 1EC: 0
>sp|Q94ID7|GGPPS_HEVBR Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Hevea brasiliensis GN=GGPS PE=1 SV=1 Back     alignment and function description
>sp|Q43133|GGPPS_SINAL Geranylgeranyl pyrophosphate synthase, chloroplastic/chromoplastic OS=Sinapis alba GN=GGPS1 PE=1 SV=1 Back     alignment and function description
>sp|P34802|GGPP1_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic OS=Arabidopsis thaliana GN=GGPPS1 PE=1 SV=2 Back     alignment and function description
>sp|Q9LUD9|GGPP3_ARATH Geranylgeranyl pyrophosphate synthase 3, chloroplastic OS=Arabidopsis thaliana GN=GGPP3 PE=2 SV=1 Back     alignment and function description
>sp|Q9ZU77|GGPP7_ARATH Geranylgeranyl pyrophosphate synthase 7, chloroplastic OS=Arabidopsis thaliana GN=At2g18620 PE=2 SV=1 Back     alignment and function description
>sp|P80042|GGPPS_CAPAN Geranylgeranyl pyrophosphate synthase, chloroplastic OS=Capsicum annuum GN=GGPS1 PE=3 SV=1 Back     alignment and function description
>sp|Q9LRR0|GGPP8_ARATH Putative geranylgeranyl pyrophosphate synthase 8, chloroplastic OS=Arabidopsis thaliana GN=At3g14510 PE=5 SV=2 Back     alignment and function description
>sp|Q9LUE1|GGPP9_ARATH Geranylgeranyl pyrophosphate synthase 9, chloroplastic OS=Arabidopsis thaliana GN=GGPPS9 PE=1 SV=1 Back     alignment and function description
>sp|O04046|GGPP2_ARATH Heterodimeric geranylgeranyl pyrophosphate synthase large subunit 2 OS=Arabidopsis thaliana GN=GGPPS2 PE=1 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query170
255580739 372 geranyl geranyl pyrophosphate synthase, 0.976 0.446 0.568 2e-51
325516280 365 geranylgeranyl pyrophosphate synthase 1 0.982 0.457 0.535 7e-50
350538439 365 geranylgeranyl pyrophosphate synthase 1 0.982 0.457 0.535 2e-49
290575616 365 geranylgeranyl diphosphate synthase [Nic 0.982 0.457 0.547 4e-49
291170333 370 geranylgeranyl diphosphate synthase [Jat 0.976 0.448 0.532 8e-48
224069444 287 predicted protein [Populus trichocarpa] 0.976 0.578 0.502 6e-45
224069436 314 predicted protein [Populus trichocarpa] 0.952 0.515 0.539 7e-45
224077270 365 predicted protein [Populus trichocarpa] 0.976 0.454 0.508 7e-44
4958920 367 GGPP synthase [Daucus carota] 0.976 0.452 0.494 2e-43
374639387 346 geranylgeranyl diphosphate synthase 2 [S 0.982 0.482 0.511 4e-43
>gi|255580739|ref|XP_002531191.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis] gi|223529232|gb|EEF31206.1| geranyl geranyl pyrophosphate synthase, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  206 bits (524), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 95/167 (56%), Positives = 130/167 (77%), Gaps = 1/167 (0%)

Query: 3   TKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEAS 62
           TKNVSPDR++RAI E+ SA+GSEGL AGQI+DI SEGKDVS+S+L +IH HK+ K +EAS
Sbjct: 206 TKNVSPDRVVRAIAELGSAVGSEGLVAGQIVDIDSEGKDVSVSDLEYIHIHKTAKLLEAS 265

Query: 63  IVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVI-GSPETKETTGRDMLRGKATY 121
           +V G I+GG ++E +ER+R Y +C+G+ +Q+ +DI+DV   S E  +T G+D++  KATY
Sbjct: 266 VVCGAILGGADDESVERVRKYARCIGLLFQVVDDILDVTKSSEELGKTAGKDLITDKATY 325

Query: 122 PKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN 168
           PKL+GIDE++  A +L+ +A QELAYFD AKAAPL H  N++ S  N
Sbjct: 326 PKLMGIDEARKLAAKLVDQANQELAYFDSAKAAPLYHFANYIASRQN 372

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|325516280|gb|ADZ24718.1| geranylgeranyl pyrophosphate synthase 1 [Solanum pennellii] Back     alignment and taxonomy information
>gi|350538439|ref|NP_001234087.1| geranylgeranyl pyrophosphate synthase 1 [Solanum lycopersicum] gi|82547880|gb|ABB82554.1| geranylgeranyl pyrophosphate synthase 1 [Solanum lycopersicum] Back     alignment and taxonomy information
>gi|290575616|gb|ADD49735.1| geranylgeranyl diphosphate synthase [Nicotiana tabacum] Back     alignment and taxonomy information
>gi|291170333|gb|ADD82422.1| geranylgeranyl diphosphate synthase [Jatropha curcas] Back     alignment and taxonomy information
>gi|224069444|ref|XP_002302978.1| predicted protein [Populus trichocarpa] gi|222844704|gb|EEE82251.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224069436|ref|XP_002302977.1| predicted protein [Populus trichocarpa] gi|222844703|gb|EEE82250.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224077270|ref|XP_002305196.1| predicted protein [Populus trichocarpa] gi|222848160|gb|EEE85707.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|4958920|dbj|BAA78047.1| GGPP synthase [Daucus carota] Back     alignment and taxonomy information
>gi|374639387|gb|AEZ55682.1| geranylgeranyl diphosphate synthase 2 [Salvia miltiorrhiza] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query170
TAIR|locus:2115450371 GGPS1 "geranylgeranyl pyrophos 0.958 0.439 0.401 1e-29
TAIR|locus:2093832357 AT3G29430 [Arabidopsis thalian 0.958 0.456 0.377 7.1e-29
UNIPROTKB|P80042369 GGPS1 "Geranylgeranyl pyrophos 0.976 0.449 0.386 9.1e-29
TAIR|locus:2089626360 AT3G14530 "AT3G14530" [Arabido 0.958 0.452 0.383 9.1e-29
TAIR|locus:2046283347 AT2G18620 [Arabidopsis thalian 0.958 0.469 0.389 1.9e-28
TAIR|locus:2079028360 AT3G32040 [Arabidopsis thalian 0.958 0.452 0.365 6.4e-28
TAIR|locus:2048993376 GGPS2 "geranylgeranyl pyrophos 0.970 0.438 0.384 3.5e-27
TAIR|locus:2087550344 AT3G20160 [Arabidopsis thalian 0.952 0.470 0.372 4.5e-27
TAIR|locus:2046258372 GGPS4 "geranylgeranyl pyrophos 0.947 0.432 0.363 4.5e-27
TAIR|locus:2010182336 GGPS6 "geranylgeranyl pyrophos 0.958 0.485 0.360 4e-26
TAIR|locus:2115450 GGPS1 "geranylgeranyl pyrophosphate synthase 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 67/167 (40%), Positives = 104/167 (62%)

Query:     6 VSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEG---KDVSLSELNFIHRHKSEKFVEAX 62
             VSP R++RA+ E++ AIG+EGL AGQ++DISSEG    DV L  L FIH HK+   +EA 
Sbjct:   205 VSPVRVVRAVGELAKAIGTEGLVAGQVVDISSEGLDLNDVGLEHLEFIHLHKTAALLEAS 264

Query:    63 XXXXXXXXXXXXXXXXRMRNYGKCVGMAYQLWNDIVDVI-GSPETKETTGRDMLRGKATY 121
                             R+R + +C+G+ +Q+ +DI+DV   S E  +T G+D++  K TY
Sbjct:   265 AVLGAIVGGGSDDEIERLRKFARCIGLLFQVVDDILDVTKSSKELGKTAGKDLIADKLTY 324

Query:   122 PKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN 168
             PK++G+++S+ +A++L  +A+ +L  FD  K APL  L N++    N
Sbjct:   325 PKIMGLEKSREFAEKLNREARDQLLGFDSDKVAPLLALANYIAYRQN 371
GO:0008299 "isoprenoid biosynthetic process" evidence=IEA;TAS
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0004311 "farnesyltranstransferase activity" evidence=IDA
GO:0009513 "etioplast" evidence=IDA
GO:0004161 "dimethylallyltranstransferase activity" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0019761 "glucosinolate biosynthetic process" evidence=RCA
TAIR|locus:2093832 AT3G29430 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P80042 GGPS1 "Geranylgeranyl pyrophosphate synthase, chloroplastic" [Capsicum annuum (taxid:4072)] Back     alignment and assigned GO terms
TAIR|locus:2089626 AT3G14530 "AT3G14530" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2046283 AT2G18620 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2079028 AT3G32040 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2048993 GGPS2 "geranylgeranyl pyrophosphate synthase 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2087550 AT3G20160 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2046258 GGPS4 "geranylgeranyl pyrophosphate synthase 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010182 GGPS6 "geranylgeranyl pyrophosphate synthase 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
4th Layer2.5.1.10LOW CONFIDENCE prediction!
3rd Layer2.5.1LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
gw1.II.860.1
hypothetical protein (306 aa)
(Populus trichocarpa)
Predicted Functional Partners:
IDI
SubName- Full=Putative chloroplast isopentenyl diphosphate isomerase; EC=5.3.3.2; Flags- Fragme [...] (234 aa)
•    •• 0.908
fgenesh4_pm.C_LG_IX000553
hypothetical protein (234 aa)
     •• 0.906
eugene3.00012780
annotation not avaliable (326 aa)
  •  • •0.906
gw1.I.925.1
hypothetical protein (242 aa)
     •• 0.906
estExt_fgenesh4_pg.C_280076
dimethylallyltranstransferase (321 aa)
  •  •••0.906
eugene3.00101320
dimethylallyltranstransferase (383 aa)
  •  •••0.905
grail3.0045022601
hypothetical protein (259 aa)
  •  • •0.904
gw1.XV.832.1
hypothetical protein (236 aa)
  •  • •0.904
grail3.0001025501
hypothetical protein (314 aa)
  •  • •0.903
gw1.VII.3333.1
annotation not avaliable (311 aa)
  •  •••0.902

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query170
cd00685259 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphat 2e-32
COG0142322 COG0142, IspA, Geranylgeranyl pyrophosphate syntha 4e-32
pfam00348260 pfam00348, polyprenyl_synt, Polyprenyl synthetase 6e-29
cd00867236 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S 4e-28
PRK10581299 PRK10581, PRK10581, geranyltranstransferase; Provi 6e-28
cd00385243 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth 6e-16
CHL00151323 CHL00151, preA, prenyl transferase; Reviewed 2e-14
PRK10888323 PRK10888, PRK10888, octaprenyl diphosphate synthas 1e-06
TIGR02748319 TIGR02748, GerC3_HepT, heptaprenyl diphosphate syn 1e-06
PLN02857416 PLN02857, PLN02857, octaprenyl-diphosphate synthas 1e-04
TIGR02749322 TIGR02749, prenyl_cyano, solanesyl diphosphate syn 0.002
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information 
 Score =  115 bits (291), Expect = 2e-32
 Identities = 52/159 (32%), Positives = 84/159 (52%), Gaps = 10/159 (6%)

Query: 11  LLRAIVEMSSAIGSEGLAAGQIMDISSEGK-DVSLSELNFIHRHKSEKFVEASIVSGVII 69
             RA+   S AI    L  GQ++D+ SE   DV+  E   I R K+     A+ + G ++
Sbjct: 106 YPRALELFSEAI--LELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALL 163

Query: 70  GGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPET--KETTGRDMLRGKATYPKLVGI 127
            G +EEE E ++ +G+ +G+A+Q+ +DI+D+ G PET  K   G D+  GK T P L+ +
Sbjct: 164 AGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGK-PVGSDLREGKCTLPVLLAL 222

Query: 128 DESKNYAKELLAKAKQELAYFDPAKA-APLDHLVNFMVS 165
              +  A+E   KA + L     + A   L  L +F++ 
Sbjct: 223 ---RELAREYEEKALEALKALPESPAREALRALADFILE 258

These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya. Length = 259
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase Back     alignment and domain information
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional Back     alignment and domain information
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed Back     alignment and domain information
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component II Back     alignment and domain information
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase Back     alignment and domain information
>gnl|CDD|131796 TIGR02749, prenyl_cyano, solanesyl diphosphate synthase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 170
PRK10581299 geranyltranstransferase; Provisional 100.0
PLN02890422 geranyl diphosphate synthase 100.0
COG0142322 IspA Geranylgeranyl pyrophosphate synthase [Coenzy 100.0
PRK10888323 octaprenyl diphosphate synthase; Provisional 100.0
TIGR02748319 GerC3_HepT heptaprenyl diphosphate synthase compon 100.0
TIGR02749322 prenyl_cyano solanesyl diphosphate synthase. Membe 100.0
CHL00151323 preA prenyl transferase; Reviewed 100.0
PLN02857416 octaprenyl-diphosphate synthase 100.0
cd00685259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 99.98
KOG0776384 consensus Geranylgeranyl pyrophosphate synthase/Po 99.97
PF00348260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 99.96
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. 99.94
KOG0777322 consensus Geranylgeranyl pyrophosphate synthase/Po 99.79
KOG0711347 consensus Polyprenyl synthetase [Coenzyme transpor 99.55
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym 99.51
PLN02632334 phytoene synthase 97.52
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase 97.47
TIGR03465266 HpnD squalene synthase HpnD. The genes of this fam 97.44
TIGR03464266 HpnC squalene synthase HpnC. This family of genes 97.32
PF00494267 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR 96.87
TIGR01559336 squal_synth farnesyl-diphosphate farnesyltransfera 96.82
PF03936270 Terpene_synth_C: Terpene synthase family, metal bi 93.93
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolis 93.81
cd00687303 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cycl 93.58
cd00868284 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terp 91.09
TIGR02748 319 GerC3_HepT heptaprenyl diphosphate synthase compon 89.71
PRK10888 323 octaprenyl diphosphate synthase; Provisional 89.42
cd00684542 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, C 88.58
PRK12872285 ubiA prenyltransferase; Reviewed 88.37
cd00685 259 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthase 87.35
PRK13105282 ubiA prenyltransferase; Reviewed 85.62
PF00348 260 polyprenyl_synt: Polyprenyl synthetase; InterPro: 85.24
PRK12884279 ubiA prenyltransferase; Reviewed 84.74
PF0678385 UPF0239: Uncharacterised protein family (UPF0239); 82.92
PRK13591307 ubiA prenyltransferase; Provisional 82.09
TIGR02749 322 prenyl_cyano solanesyl diphosphate synthase. Membe 81.19
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information 
Probab=100.00  E-value=6.5e-37  Score=253.85  Aligned_cols=163  Identities=32%  Similarity=0.611  Sum_probs=150.2

Q ss_pred             CCHHHHHHHHHHHHHhhchhhhhhhhHHhhhcCCCCCCHHHHHHHHHccHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHH
Q 042175            6 VSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGGGNE-EEIERMRNYG   84 (170)
Q Consensus         6 ~~~~~~~~~i~~l~~~~g~~~l~~GQ~~dl~~~~~~~~~~~~~~i~~~KTg~L~~~~~~~ga~lag~~~-~~~~~l~~~g   84 (170)
                      .++.++.++++.++++.|..+|+.||.+|+.+....+++++|.+|+..|||+||++||++|++++|.++ +..+.+++||
T Consensus       133 ~~~~~~~~~~~~~~~~~~~~~l~~GQ~ld~~~~~~~~~~~~y~~i~~~KTa~L~~~~~~~gailag~~~~~~~~~l~~~g  212 (299)
T PRK10581        133 VSDRDRISMISELASASGIAGMCGGQALDLEAEGKQVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYA  212 (299)
T ss_pred             CChHHHHHHHHHHHHhcccchhhHhhHHHHhccCCCCCHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHH
Confidence            355667889999999877799999999999987666899999999999999999999999999999864 5789999999


Q ss_pred             HHHHHHHhHHhhhhhccCCC-CCCCccchHhhhCCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCC-C-hHHHHHHHH
Q 042175           85 KCVGMAYQLWNDIVDVIGSP-ETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPA-K-AAPLDHLVN  161 (170)
Q Consensus        85 ~~lG~afQi~DDilD~~~~~-~~gk~~~~D~~~gk~t~~~l~~~e~a~~~~~~~~~~a~~~L~~l~~~-~-~~~L~~l~~  161 (170)
                      +++|+||||+||++|+++++ .+||+.++|+++||+|||+++|++++++.+++|.++|++.|+.+|+. . ++.|.+|++
T Consensus       213 ~~lG~aFQI~DDilD~~g~~~~~GK~~g~Dl~~gk~T~p~l~~~e~a~~~a~~~~~~A~~~l~~l~~~~~~~~~L~~l~~  292 (299)
T PRK10581        213 ESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLDQLAAQSLDTSALEALAN  292 (299)
T ss_pred             HHHHHHHHHHHHHccccCChHHHCCCcchhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCchhHHHHHHHHH
Confidence            99999999999999999998 99999999999999999999999999999999999999999999753 3 578999999


Q ss_pred             HHHhccc
Q 042175          162 FMVSFDN  168 (170)
Q Consensus       162 ~~~~r~~  168 (170)
                      |+.+|.+
T Consensus       293 ~~~~R~~  299 (299)
T PRK10581        293 YIIQRDK  299 (299)
T ss_pred             HHHhccC
Confidence            9999964

>PLN02890 geranyl diphosphate synthase Back     alignment and domain information
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism] Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information
>CHL00151 preA prenyl transferase; Reviewed Back     alignment and domain information
>PLN02857 octaprenyl-diphosphate synthase Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>KOG0776 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases Back     alignment and domain information
>KOG0777 consensus Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information
>KOG0711 consensus Polyprenyl synthetase [Coenzyme transport and metabolism] Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1 Back     alignment and domain information
>PLN02632 phytoene synthase Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>TIGR03465 HpnD squalene synthase HpnD Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information
>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2 Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase Back     alignment and domain information
>PF03936 Terpene_synth_C: Terpene synthase family, metal binding domain; InterPro: IPR005630 Sequences containing this domain belong to the terpene synthase family Back     alignment and domain information
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1 Back     alignment and domain information
>cd00868 Terpene_cyclase_C1 Terpene cyclases, Class 1 Back     alignment and domain information
>TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1 Back     alignment and domain information
>PRK12872 ubiA prenyltransferase; Reviewed Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail Back     alignment and domain information
>PRK13105 ubiA prenyltransferase; Reviewed Back     alignment and domain information
>PF00348 polyprenyl_synt: Polyprenyl synthetase; InterPro: IPR000092 A variety of isoprenoid compounds are synthesized by various organisms Back     alignment and domain information
>PRK12884 ubiA prenyltransferase; Reviewed Back     alignment and domain information
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function Back     alignment and domain information
>PRK13591 ubiA prenyltransferase; Provisional Back     alignment and domain information
>TIGR02749 prenyl_cyano solanesyl diphosphate synthase Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query170
3kra_A295 Mint Heterotetrameric Geranyl Pyrophosphate Synthas 6e-32
2j1p_A293 Geranylgeranyl Diphosphate Synthase From Sinapis Al 7e-28
2j1o_A268 Geranylgeranyl Diphosphate Synthase From Sinapis Al 2e-25
4f62_A317 Crystal Structure Of A Putative Farnesyl-Diphosphat 1e-17
1rqi_A300 Active Conformation Of Farnesyl Pyrophosphate Synth 1e-17
1rqj_A299 Active Conformation Of Farnesyl Pyrophosphate Synth 1e-17
2for_A323 Crystal Structure Of The Shigella Flexneri Farnesyl 2e-17
3ts7_A324 Crystal Structure Of Farnesyl Diphosphate Synthase 3e-13
3p41_A303 Crystal Structure Of Polyprenyl Synthetase From Pse 5e-13
3lji_A304 Crystal Structure Of Putative Geranyltranstransfera 5e-13
3p8r_A302 Crystal Structure Of Polyprenyl Synthase From Vibri 4e-12
3uca_A324 Crystal Structure Of Isoprenoid Synthase (Target Ef 7e-11
3m9u_A309 Crystal Structure Of Geranylgeranyl Pyrophosphate S 1e-10
3q1o_A310 Crystal Structure Of Geranyltransferase From Helico 1e-09
3llw_A311 Crystal Structure Of Geranyltransferase From Helico 1e-09
3npk_A291 The Crystal Structure Of Geranyltranstransferase Fr 3e-09
3p8l_A302 Crystal Structure Of Polyprenyl Synthase From Enter 5e-09
1rtr_A301 Crystal Structure Of S. Aureus Farnesyl Pyrophospha 6e-09
3rmg_A334 Crystal Structure Of Geranylgeranyl Pyrophosphate S 5e-06
3lvs_A298 Crystal Structure Of Farnesyl Diphosphate Synthase 6e-06
3m0g_A297 Crystal Structure Of Putative Farnesyl Diphosphate 2e-05
3oyr_A345 Crystal Structure Of Polyprenyl Synthase From Caulo 6e-05
3lmd_A360 Crystal Structure Of Geranylgeranyl Pyrophosphate S 1e-04
3aqb_B325 M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphospha 2e-04
2h8o_A335 The 1.6a Crystal Structure Of The Geranyltransferas 6e-04
1wy0_A342 Crystal Structure Of Geranylgeranyl Pyrophosphate S 7e-04
>pdb|3KRA|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In Complex With Magnesium Length = 295 Back     alignment and structure 
Iteration: 1

 Score =  133 bits (334), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 63/168 (37%), Positives = 103/168 (61%), Gaps = 2/168 (1%)
Query: 3   TKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEG-KDVSLSELNFIHRHKSEKFVEA 61
           TK   P+R++R + E++ +IGSEGL AGQ++D+ SEG  +V L  L FIH HK+   ++ 
Sbjct: 128 TKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQG 187
Query: 62  XXXXXXXXXXXXXXXXXRMRNYGKCVGMAYQLWNDIVDVI-GSPETKETTGRDMLRGKAT 120
                            ++R +  C+G+ +Q+ +DI+DV   S E  +T G+D++  K T
Sbjct: 188 SVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTKSSKELGKTAGKDLVADKTT 247
Query: 121 YPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNFMVSFDN 168
           YPKL+G+++SK +A  L  +A+++L +F P +AAPL  L N++   DN
Sbjct: 248 YPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 295
>pdb|2J1P|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In Complex With Ggpp Length = 293 Back     alignment and structure
>pdb|2J1O|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba Length = 268 Back     alignment and structure
>pdb|4F62|A Chain A, Crystal Structure Of A Putative Farnesyl-Diphosphate Synthase From Marinomonas Sp. Med121 (Target Efi-501980) Length = 317 Back     alignment and structure
>pdb|1RQI|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase Bound To Isopentyl Pyrophosphate And Dimethylallyl S- Thiolodiphosphate Length = 300 Back     alignment and structure
>pdb|1RQJ|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase Bound To Isopentyl Pyrophosphate And Risedronate Length = 299 Back     alignment and structure
>pdb|2FOR|A Chain A, Crystal Structure Of The Shigella Flexneri Farnesyl Pyrophosphate Synthase Complex With An Isopentenyl Pyrophosphate Length = 323 Back     alignment and structure
>pdb|3TS7|A Chain A, Crystal Structure Of Farnesyl Diphosphate Synthase (Target Efi-501951) From Methylococcus Capsulatus Length = 324 Back     alignment and structure
>pdb|3P41|A Chain A, Crystal Structure Of Polyprenyl Synthetase From Pseudomonas Fluorescens Pf-5 Complexed With Magnesium And Isoprenyl Pyrophosphate Length = 303 Back     alignment and structure
>pdb|3LJI|A Chain A, Crystal Structure Of Putative Geranyltranstransferase From Pseudomonas Fluorescens Pf-5 Length = 304 Back     alignment and structure
>pdb|3P8R|A Chain A, Crystal Structure Of Polyprenyl Synthase From Vibrio Cholerae Length = 302 Back     alignment and structure
>pdb|3UCA|A Chain A, Crystal Structure Of Isoprenoid Synthase (Target Efi-501974) From Clostridium Perfringens Length = 324 Back     alignment and structure
>pdb|3M9U|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase From Lactobacillus Brevis Atcc 367 Length = 309 Back     alignment and structure
>pdb|3Q1O|A Chain A, Crystal Structure Of Geranyltransferase From Helicobacter Pylori Complexed With Magnesium And Isoprenyl Diphosphate Length = 310 Back     alignment and structure
>pdb|3LLW|A Chain A, Crystal Structure Of Geranyltransferase From Helicobacter Pylori 26695 Length = 311 Back     alignment and structure
>pdb|3NPK|A Chain A, The Crystal Structure Of Geranyltranstransferase From Campylobacter Jejuni Length = 291 Back     alignment and structure
>pdb|3P8L|A Chain A, Crystal Structure Of Polyprenyl Synthase From Enterococcus Faecalis V583 Length = 302 Back     alignment and structure
>pdb|1RTR|A Chain A, Crystal Structure Of S. Aureus Farnesyl Pyrophosphate Synthase Length = 301 Back     alignment and structure
>pdb|3RMG|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase From Bacteroides Thetaiotaomicron Length = 334 Back     alignment and structure
>pdb|3LVS|A Chain A, Crystal Structure Of Farnesyl Diphosphate Synthase From Rhodobacter Capsulatus Sb1003 Length = 298 Back     alignment and structure
>pdb|3M0G|A Chain A, Crystal Structure Of Putative Farnesyl Diphosphate Synthase From Rhodobacter Capsulatus Length = 297 Back     alignment and structure
>pdb|3OYR|A Chain A, Crystal Structure Of Polyprenyl Synthase From Caulobacter Crescentus Cb15 Complexed With Calcium And Isoprenyl Diphosphate Length = 345 Back     alignment and structure
>pdb|3LMD|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Atcc 13032 Length = 360 Back     alignment and structure
>pdb|3AQB|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase In Complex With Magnesium Length = 325 Back     alignment and structure
>pdb|2H8O|A Chain A, The 1.6a Crystal Structure Of The Geranyltransferase From Agrobacterium Tumefaciens Length = 335 Back     alignment and structure
>pdb|1WY0|A Chain A, Crystal Structure Of Geranylgeranyl Pyrophosphate Synthetase From Pyrococcus Horikoshii Ot3 Length = 342 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query170
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 6e-61
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 9e-61
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 4e-60
4f62_A317 Geranyltranstransferase; enzyme function initiativ 6e-60
3lsn_A304 Geranyltranstransferase; structural genomics, prot 6e-60
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 4e-58
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 5e-58
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 1e-57
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 2e-57
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 3e-57
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 1e-56
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 2e-56
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 3e-56
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 5e-55
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 2e-54
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 1e-43
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 5e-35
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 7e-30
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 4e-29
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 1e-24
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 3e-24
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 7e-23
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 3e-22
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 2e-20
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 1e-17
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 1e-17
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 5e-17
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 2e-16
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 2e-16
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 2e-16
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 2e-16
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 1e-15
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 2e-14
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 7e-14
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 9e-14
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 1e-13
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 2e-13
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 5e-13
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 1e-12
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 3e-12
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 3e-11
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 9e-11
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 5e-09
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Length = 301 Back     alignment and structure
 Score =  189 bits (483), Expect = 6e-61
 Identities = 42/170 (24%), Positives = 80/170 (47%), Gaps = 4/170 (2%)

Query: 2   KTKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEA 61
               ++ +  ++ +  +S A G  G+  GQ++D+ SEG+ + L  L  IH+ K+   +  
Sbjct: 125 SDDRLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDLETLEMIHKTKTGALLTF 184

Query: 62  SIVSGVIIGGGNEEEIERMRNYGKCVGMAYQLWNDIVDVIGSPET--KETTGRDMLRGKA 119
           +++S   I   ++   E + +Y   +GM +Q+ +D++D  G      K   G D+   K+
Sbjct: 185 AVMSAADIANVDDTTKEHLESYSYHLGMMFQIKDDLLDCYGDEAKLGK-KVGSDLENNKS 243

Query: 120 TYPKLVGIDESKNYAKELLAKAKQELAYFD-PAKAAPLDHLVNFMVSFDN 168
           TY  L+G D +++        A  EL   D       L  +V+   S D+
Sbjct: 244 TYVSLLGKDGAEDKLTYHRDAAVDELTQIDEQFNTKHLLEIVDLFYSRDH 293
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Length = 335 Back     alignment and structure
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Length = 324 Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Length = 317 Back     alignment and structure
>3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* 3p41_A* Length = 304 Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Length = 309 Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Length = 324 Back     alignment and structure
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A* Length = 299 Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Length = 302 Back     alignment and structure
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A 3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A* Length = 293 Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} Length = 302 Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Length = 313 Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Length = 291 Back     alignment and structure
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Length = 311 Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Length = 297 Back     alignment and structure
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Length = 274 Back     alignment and structure
>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus} Length = 273 Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Length = 352 Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Length = 284 Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Length = 342 Back     alignment and structure
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} Length = 285 Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Length = 380 Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Length = 295 Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} Length = 358 Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Length = 334 Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Length = 330 Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A* Length = 360 Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Length = 334 Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Length = 345 Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Length = 325 Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Length = 341 Back     alignment and structure
>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices fold, chroloplast, TRAN isoprenoid biosynthetic process; 2.60A {Arabidopsis thaliana} PDB: 3aq0_A* Length = 348 Back     alignment and structure
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A {Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A* 1ubx_A* 1fps_A Length = 367 Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Length = 289 Back     alignment and structure
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, bisphosphonate, dimethyl ALLY pyrophosphate sulfate, FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma cruzi} PDB: 1yhk_A* 1yhm_A* 3iba_A* 3ick_A* 3icm_A* 3icn_A* 3icz_A* 3id0_A* Length = 362 Back     alignment and structure
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase, structural genomics, structural GEN consortium, SGC, transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F* 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ... Length = 374 Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Length = 299 Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Length = 315 Back     alignment and structure
>3dyh_A Farnesyl pyrophosphate synthase; protein-bisphosphonate complex, isoprene biosynthesis, transferase; HET: 721; 1.94A {Trypanosoma brucei} PDB: 2ewg_A* 2i19_A* 2p1c_A* 3dyf_A* 3dyg_A* 2ogd_A* 3efq_A* 3egt_A* Length = 390 Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural GENO structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Length = 301 Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Length = 340 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query170
4f62_A317 Geranyltranstransferase; enzyme function initiativ 100.0
3ts7_A324 Geranyltranstransferase; isoprenoid synthesis, far 100.0
3p8l_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
3lsn_A304 Geranyltranstransferase; structural genomics, prot 100.0
3uca_A324 Geranyltranstransferase; isoprenoid synthesis, iso 100.0
3p8r_A302 Geranyltranstransferase; isoprenyl synthase, struc 100.0
1rtr_A301 Geranyltranstransferase; 2.50A {Staphylococcus aur 100.0
2h8o_A335 Geranyltranstransferase; geranyltransferase,agroba 100.0
3lom_A313 Geranyltranstransferase; geranyltransferase, struc 100.0
1rqj_A299 Geranyltranstransferase; bisphosphonate, isoprenyl 100.0
3m0g_A297 Farnesyl diphosphate synthase; structural genomics 100.0
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphospha 100.0
3llw_A311 Geranyltranstransferase (ISPA); structural genomic 100.0
3npk_A291 Geranyltranstransferase; isoprene biosynthesis, SG 100.0
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 100.0
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 100.0
3apz_A348 Geranyl diphosphate synthase; prenyltransferase, a 100.0
3mzv_A341 Decaprenyl diphosphate synthase; transferase, stru 100.0
3rmg_A334 Octaprenyl-diphosphate synthase; structural genomi 100.0
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
3pko_A334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 100.0
4dhd_A358 Polyprenyl synthetase; isoprenoid synthesis, isopr 100.0
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosph 100.0
2ftz_A284 Geranyltranstransferase; TM0161, structural GE joi 100.0
3aqb_B325 Component B of hexaprenyl diphosphate synthase; pr 100.0
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural 100.0
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, he 100.0
2j1p_A293 Geranylgeranyl pyrophosphate synthetase; transfera 100.0
3tc1_A315 Octaprenyl pyrophosphate synthase; all alpha-helic 100.0
1wmw_A330 Geranylgeranyl diphosphate synthetase; GGPP, preny 100.0
1yhl_A362 Farnesyl pyrophosphate synthase; farnesyl diphosph 100.0
2qis_A374 Farnesyl pyrophosphate synthetase; trans-prenyltra 100.0
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, i 100.0
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 99.98
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltra 99.98
2ihi_A395 Pyrophosphate synthase; PV092040, structural genom 99.97
3dyh_A390 Farnesyl pyrophosphate synthase; protein-bisphosph 99.97
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyl 99.97
3mav_A395 Farnesyl pyrophosphate synthase; PV092040, structu 99.97
2her_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 99.97
2azj_A289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 99.96
2q58_A368 Fragment, farnesyl pyrophosphate synthase; farnesy 99.95
3kra_B274 Geranyl diphosphate synthase small subunit; prenyl 99.92
3qkc_B273 Geranyl diphosphate synthase small subunit; struct 99.9
4fp4_A285 Polyprenyl synthetase; isoprenoid synthesis, isopr 99.87
3acx_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynt 96.98
3vj8_A343 Squalene synthase; farnesyl-diphosphate farnesyltr 96.87
4hd1_A294 Squalene synthase HPNC; MCSG, structural genomics, 96.85
3kb9_A382 EPI-isozizaene synthase; terpenoid cyclase, alpha- 94.44
1ps1_A337 Pentalenene synthase; antibiotic biosynthesis, ses 94.16
3g4d_A554 (+)-delta-cadinene synthase isozyme XC1; cyclase, 91.75
3n0f_A555 Isoprene synthase; terpene cyclase fold, hemiterpe 90.74
3m00_A550 Aristolochene synthase; plant terpenoid cyclase, l 90.64
1di1_A300 Aristolochene synthase; sesquiterpene cyclase, iso 90.39
3rmg_A 334 Octaprenyl-diphosphate synthase; structural genomi 90.3
3mzv_A 341 Decaprenyl diphosphate synthase; transferase, stru 90.22
4fp4_A 285 Polyprenyl synthetase; isoprenoid synthesis, isopr 89.97
3v1v_A433 2-MIB synthase, 2-methylisoborneol synthase; class 89.18
3pko_A 334 Geranylgeranyl pyrophosphate synthase; isoprenyl d 87.92
2ong_A543 4S-limonene synthase; monoterpene synthase, monote 87.76
2q80_A 301 Geranylgeranyl pyrophosphate synthetase; isoprenoi 87.08
4f62_A 317 Geranyltranstransferase; enzyme function initiativ 86.75
3bny_A320 Aristolochene synthase; sesquiterpene cyclase, iso 86.59
2e8v_A 340 Geranylgeranyl pyrophosphate synthetase; prenyltra 86.17
3aqb_B 325 Component B of hexaprenyl diphosphate synthase; pr 86.06
3lmd_A 360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 85.79
3m0g_A 297 Farnesyl diphosphate synthase; structural genomics 85.64
3nf2_A 352 Putative polyprenyl synthetase; isoprenyl diphosph 85.21
2ftz_A 284 Geranyltranstransferase; TM0161, structural GE joi 85.11
1v4e_A 299 Octoprenyl-diphosphate synthase; trans-type prenyl 83.89
1wy0_A 342 Geranylgeranyl pyrophosphate synthetase; pyrococcu 83.54
2azj_A 289 Geranylgeranyl pyrophosphate synthetase; hexpps, t 82.58
3oyr_A 345 Trans-isoprenyl diphosphate synthase; isoprenyl sy 82.43
3pde_A 309 Farnesyl-diphosphate synthase; isoprenyl diphospha 82.05
3p8l_A 302 Geranyltranstransferase; isoprenyl synthase, struc 81.76
1n1b_A549 (+)-bornyl diphosphate synthase; terpene synthase 81.39
4dhd_A 358 Polyprenyl synthetase; isoprenoid synthesis, isopr 81.37
1wmw_A 330 Geranylgeranyl diphosphate synthetase; GGPP, preny 80.45
1rqj_A 299 Geranyltranstransferase; bisphosphonate, isoprenyl 80.38
3lsn_A 304 Geranyltranstransferase; structural genomics, prot 80.26
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Back     alignment and structure
Probab=100.00  E-value=3.5e-40  Score=273.91  Aligned_cols=164  Identities=32%  Similarity=0.578  Sum_probs=138.6

Q ss_pred             CCCHHHHHHHHHHHHHhhchhhhhhhhHHhhhcCCCCCCHHHHHHHHHccHHHHHHHHHHHHHHhcC-CCHHHHHHHHHH
Q 042175            5 NVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGG-GNEEEIERMRNY   83 (170)
Q Consensus         5 ~~~~~~~~~~i~~l~~~~g~~~l~~GQ~~dl~~~~~~~~~~~~~~i~~~KTg~L~~~~~~~ga~lag-~~~~~~~~l~~~   83 (170)
                      +++++.+.++++.+++++|..+|+.||.+|+.+.+..+++++|.+|+++|||+||++||++|++++| ++++..+.+++|
T Consensus       131 ~~~~~~~~~~i~~la~a~g~~~m~~GQ~lDl~~~~~~~t~~~y~~i~~~KTg~L~~~a~~~Ga~lag~a~~~~~~~l~~~  210 (317)
T 4f62_A          131 SAQPELAIKLIQELVVASGRNGMITGQMIDLSSENKNISLAELEQMHVHKTGALIKASVRMGALSTGQVKPEQLAKLDAY  210 (317)
T ss_dssp             CCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTSSSCCCHHHHHHHHHHHTHHHHHHHHHHHHHTTTCCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhhhHHHhHHHHHhccCCCCCHHHHHHHHHhchHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            4577888999999999998889999999999998767999999999999999999999999999999 899999999999


Q ss_pred             HHHHHHHHhHHhhhhhccCCC-CCCCccchHhhhCCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHH
Q 042175           84 GKCVGMAYQLWNDIVDVIGSP-ETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDPAKAAPLDHLVNF  162 (170)
Q Consensus        84 g~~lG~afQi~DDilD~~~~~-~~gk~~~~D~~~gk~t~~~l~~~e~a~~~~~~~~~~a~~~L~~l~~~~~~~L~~l~~~  162 (170)
                      |.+||+||||+||++|+++++ ..||+.++|+++||+|||+++|+++|++.+++|.++|++.|+.||+ .++.|.+|++|
T Consensus       211 g~~lGlAFQI~DDiLD~~gd~~~~GK~~g~Dl~egK~T~p~l~gle~a~~~a~~~~~~A~~~L~~l~~-~~~~L~~l~~~  289 (317)
T 4f62_A          211 AHAIGLAFQVQDDIIDLTSDTETLGKTQFSDAEANKATYPKLLGLDGAKALVVRLHEQAIAQISEFGD-KSQPLTDLANY  289 (317)
T ss_dssp             HHHHHHHHHHHHHHHHTC----------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHGGGGG-GGHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccCChHhhCCCcchHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-hHHHHHHHHHH
Confidence            999999999999999999998 9999999999999999999999999999999999999999999986 67899999999


Q ss_pred             HHhcccC
Q 042175          163 MVSFDNV  169 (170)
Q Consensus       163 ~~~r~~~  169 (170)
                      +.+|.+.
T Consensus       290 ~~~R~~~  296 (317)
T 4f62_A          290 IIDRNHA  296 (317)
T ss_dssp             HHC----
T ss_pred             HHHhccc
Confidence            9999764
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate synthase; 1.94A {Methylococcus capsulatus} Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Back     alignment and structure
>3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* 3p41_A* Back     alignment and structure
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid diphosphate synthase; 2.00A {Clostridium perfringens} Back     alignment and structure
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.50A {Vibrio cholerae} SCOP: a.128.1.1 Back     alignment and structure
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP: a.128.1.1 Back     alignment and structure
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium tumefaciens, structural GEN PSI-2, protein structure initiative; 1.60A {Agrobacterium tumefaciens} Back     alignment and structure
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Legionella pneumophila subsp} Back     alignment and structure
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A* Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Back     alignment and structure
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein structure initiative, nysgrc; 2.30A {Helicobacter pylori} PDB: 3q1o_A* Back     alignment and structure
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural genomics protein structure initiative; 1.50A {Campylobacter jejuni} Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Back     alignment and structure
>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices fold, chroloplast, TRAN isoprenoid biosynthetic process; 2.60A {Arabidopsis thaliana} PDB: 3aq0_A* Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A* Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative, geranylge pyrophosphate synthase; 1.90A {Corynebacterium glutamicum} PDB: 3qqv_A* Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Back     alignment and structure
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A 3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A* Back     alignment and structure
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold, transferase; 2.00A {Helicobacter pylori} Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Back     alignment and structure
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, bisphosphonate, dimethyl ALLY pyrophosphate sulfate, FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma cruzi} PDB: 1yhk_A* 1yhm_A* 3iba_A* 3ick_A* 3icm_A* 3icn_A* 3icz_A* 3id0_A* Back     alignment and structure
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase, structural genomics, structural GEN consortium, SGC, transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F* 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ... Back     alignment and structure
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A {Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A* 1ubx_A* 1fps_A Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural GENO structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>3dyh_A Farnesyl pyrophosphate synthase; protein-bisphosphonate complex, isoprene biosynthesis, transferase; HET: 721; 1.94A {Trypanosoma brucei} PDB: 2ewg_A* 2i19_A* 2p1c_A* 3dyf_A* 3dyg_A* 2ogd_A* 3efq_A* 3egt_A* Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Back     alignment and structure
>3mav_A Farnesyl pyrophosphate synthase; PV092040, structural genomics, structural genomics consortium, SGC, transferase, isoprene biosynthesis; 2.10A {Plasmodium vivax} PDB: 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A* 3ph7_A* 3rbm_A* 3ryw_A* Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>2q58_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate synthase, structural genomics, structur genomics consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium parvum} PDB: 2o1o_A* Back     alignment and structure
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase, isoprene biosynthesis, isoprenyl pyrophosphate synthase, transferase; 1.90A {Mentha x piperita} PDB: 3krc_B* 3krf_B* 3kro_B* 3krp_B* 3oab_B* 3oac_B* Back     alignment and structure
>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 2.20A {Antirrhinum majus} Back     alignment and structure
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} Back     alignment and structure
>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ... Back     alignment and structure
>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3v66_A* 3lee_A* 3q2z_A* 3q30_A* 3asx_A* 1ezf_A* Back     alignment and structure
>4hd1_A Squalene synthase HPNC; MCSG, structural genomics, PSI-biology, midwest center for S genomics, transferase; 2.40A {Alicyclobacillus acidocaldarius subsp} Back     alignment and structure
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold, farnesyl diphosphate, metal-binding, lyase, magnesium; HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A 3lgk_A 3lg5_A* Back     alignment and structure
>1ps1_A Pentalenene synthase; antibiotic biosynthesis, sesquiterpene cyclase, lyase; 2.60A {Streptomyces SP} SCOP: a.128.1.4 PDB: 1hm7_A 1hm4_A Back     alignment and structure
>3g4d_A (+)-delta-cadinene synthase isozyme XC1; cyclase, lyase, magnesium, metal-binding; 2.40A {Gossypium arboreum} PDB: 3g4f_A* Back     alignment and structure
>3n0f_A Isoprene synthase; terpene cyclase fold, hemiterpene synthase, DDXXD motif, NSE motif, lyase; 2.70A {Populus tremula x populus alba} PDB: 3n0g_A* Back     alignment and structure
>3m00_A Aristolochene synthase; plant terpenoid cyclase, lyase binding domain, (2-CIS, 6-trans)-2-fluorofarnesyl diphospha magnesium, metal-binding; HET: 2CF; 2.10A {Nicotiana tabacum} PDB: 3lz9_A* 3m02_A* 3m01_A* 5eau_A* 1hxa_A* 1hx9_A* 1hxc_A* 5eas_A 1hxg_A 4di5_A* 5eat_A* Back     alignment and structure
>1di1_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid biosynthesis, lyase; 2.50A {Penicillium roqueforti} SCOP: a.128.1.4 PDB: 1dgp_A Back     alignment and structure
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein structure initiative, isoprene biosynthesis, transferase; 2.30A {Bacteroides thetaiotaomicron} Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum calidifontis} Back     alignment and structure
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Back     alignment and structure
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus brevis} PDB: 3n3d_A Back     alignment and structure
>2ong_A 4S-limonene synthase; monoterpene synthase, monoterpene cyclase, geranyl diphosphate, 2 fluorogeranyl diphosphate linalyl diphosphate; HET: FPG BTB; 2.70A {Mentha spicata} PDB: 2onh_A* Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural GENO structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Back     alignment and structure
>4f62_A Geranyltranstransferase; enzyme function initiative, structural genomics; 2.10A {Marinomonas SP} Back     alignment and structure
>3bny_A Aristolochene synthase; sesquiterpene cyclase, isoprenoid, farnesyl diphosphate, magnesium, cyclization, lyase; HET: FPF; 1.89A {Aspergillus terreus} PDB: 2e4o_A 2oa6_A* 3bnx_A* 3cke_A* Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase, transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B* Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} PDB: 3q2q_A* Back     alignment and structure
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein structure initiative, NYSGXRC, biosynthesis, transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB: 3lvs_A Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima} Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh structural genomics, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} Back     alignment and structure
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Back     alignment and structure
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics, PSI, protein struct initiative, nysgrc; 2.00A {Enterococcus faecalis} Back     alignment and structure
>1n1b_A (+)-bornyl diphosphate synthase; terpene synthase fold, isomerase; 2.00A {Salvia officinalis} SCOP: a.102.4.1 a.128.1.3 PDB: 1n1z_A* 1n20_A* 1n21_A* 1n22_A* 1n23_A* 1n24_A* Back     alignment and structure
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate synthase, trans; 1.65A {Pyrobaculum calidifontis} PDB: 4gp1_A* 4gp2_A* Back     alignment and structure
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate synthase, structural genom riken structural genomics/proteomics initiative; 1.55A {Thermus thermophilus} Back     alignment and structure
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB: 1rqi_A* 2for_A* Back     alignment and structure
>3lsn_A Geranyltranstransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas fluorescens} PDB: 3lji_A* 3p41_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 170
d1rqja_299 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 3e-24
d1rtra_290 a.128.1.1 (A:) Farnesyl diphosphate synthase (gera 9e-20
d1v4ea_280 a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Th 3e-13
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Length = 299 Back     information, alignment and structure

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Farnesyl diphosphate synthase (geranyltranstransferase)
species: Escherichia coli [TaxId: 562]

 Score = 93.5 bits (231), Expect = 3e-24
 Identities = 50/168 (29%), Positives = 90/168 (53%), Gaps = 4/168 (2%)

Query: 2   KTKNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEA 61
               VS    +  I E++SA G  G+  GQ +D+ +EGK V L  L  IHRHK+   + A
Sbjct: 129 DMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRA 188

Query: 62  SIVSGVIIGGGNEEEIERM-RNYGKCVGMAYQLWNDIVDVIG-SPETKETTGRDMLRGKA 119
           ++  G +  G        +   Y + +G+A+Q+ +DI+DV+G +    +  G D   GK+
Sbjct: 189 AVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKS 248

Query: 120 TYPKLVGIDESKNYAKELLAKAKQELAYF--DPAKAAPLDHLVNFMVS 165
           TYP L+G+++++  A++L+  A+Q L          + L+ L ++++ 
Sbjct: 249 TYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQ 296
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Length = 290 Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Length = 280 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query170
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d1rtra_290 Farnesyl diphosphate synthase (geranyltranstransfe 100.0
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 99.97
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransfe 99.97
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga mariti 99.95
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 96 97.12
d1ps1a_311 Pentalenene synthase {Streptomyces sp., UC5319 [Ta 91.68
d2q80a1 291 Geranylgeranyl pyrophosphate synthetase {Human (Ho 89.03
d1di1a_300 Aristolochene synthase {Fungus (Penicillium roquef 83.69
d5easa2328 5-Epi-aristolochene synthase {Tobacco (Nicotiana t 81.79
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Isoprenyl diphosphate synthases
domain: Farnesyl diphosphate synthase (geranyltranstransferase)
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.6e-34  Score=236.23  Aligned_cols=165  Identities=30%  Similarity=0.597  Sum_probs=149.7

Q ss_pred             CCCCHHHHHHHHHHHHHhhchhhhhhhhHHhhhcCCCCCCHHHHHHHHHccHHHHHHHHHHHHHHhcC-CCHHHHHHHHH
Q 042175            4 KNVSPDRLLRAIVEMSSAIGSEGLAAGQIMDISSEGKDVSLSELNFIHRHKSEKFVEASIVSGVIIGG-GNEEEIERMRN   82 (170)
Q Consensus         4 ~~~~~~~~~~~i~~l~~~~g~~~l~~GQ~~dl~~~~~~~~~~~~~~i~~~KTg~L~~~~~~~ga~lag-~~~~~~~~l~~   82 (170)
                      .......+++++..++.+.|+.+|++||.+|+.+....+++++|..|+.+|||+||.+++.+|+++++ .+.+..+.+++
T Consensus       131 ~~~~~~~~~~~~~~l~~~~~~~~l~~GQ~ldl~~~~~~~~~~~~~~i~~~KT~~l~~~~~~~~a~~~~~~~~~~~~~l~~  210 (299)
T d1rqja_         131 PEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDK  210 (299)
T ss_dssp             TTCCHHHHHHHHHHHHHHHSTTTHHHHHHHHHHTTTTCCCHHHHHHHHHHHTHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhccCcccHHHHHHHHHHHHhhHHHHHHHhhhhhhcchhhHHHHHHHH
Confidence            34566778899999999988899999999999987767889999999999999999999999887654 45666788999


Q ss_pred             HHHHHHHHHhHHhhhhhccCCC-CCCCccchHhhhCCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCC--CChHHHHHH
Q 042175           83 YGKCVGMAYQLWNDIVDVIGSP-ETKETTGRDMLRGKATYPKLVGIDESKNYAKELLAKAKQELAYFDP--AKAAPLDHL  159 (170)
Q Consensus        83 ~g~~lG~afQi~DDilD~~~~~-~~gk~~~~D~~~gk~t~~~l~~~e~a~~~~~~~~~~a~~~L~~l~~--~~~~~L~~l  159 (170)
                      ||.++|+||||+||++|+++++ ..||+.++|+++||+|||++++++.+++..+++.+++.+.|+.++.  ...+.|.++
T Consensus       211 ~g~~lGiaFQi~DD~lD~~~~~~~~GK~~g~Dl~egK~Tlp~i~~le~a~~~~~~~~~~~~~~l~~l~~~~~~~~~L~~l  290 (299)
T d1rqja_         211 YAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEAL  290 (299)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCHHHHSSCTTHHHHHTCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhccchhhcCCchhhHHHCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccHHHHHHH
Confidence            9999999999999999999998 9999999999999999999999999999999999999999999864  246899999


Q ss_pred             HHHHHhccc
Q 042175          160 VNFMVSFDN  168 (170)
Q Consensus       160 ~~~~~~r~~  168 (170)
                      ++|+.+|++
T Consensus       291 ~~~i~~R~K  299 (299)
T d1rqja_         291 ADYIIQRNK  299 (299)
T ss_dssp             HHHHHHCCC
T ss_pred             HHHHHhCCC
Confidence            999999975
>d1rtra_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1di1a_ a.128.1.4 (A:) Aristolochene synthase {Fungus (Penicillium roqueforti) [TaxId: 5082]} Back     information, alignment and structure
>d5easa2 a.128.1.3 (A:221-548) 5-Epi-aristolochene synthase {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Back     information, alignment and structure